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- PDB-3n8u: Crystal structure of an imelysin peptidase (BACOVA_03801) from Ba... -

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Basic information

Entry
Database: PDB / ID: 3n8u
TitleCrystal structure of an imelysin peptidase (BACOVA_03801) from Bacteroides ovatus at 1.44 A resolution
Componentsimelysin peptidase
KeywordsHYDROLASE / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homologyImelysin-like domain / Imelysin-like domain superfamily / Imelysin / Prokaryotic membrane lipoprotein lipid attachment site profile. / Imelysin
Function and homology information
Biological speciesBacteroides ovatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.44 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: Plos One / Year: 2011
Title: Structural and sequence analysis of imelysin-like proteins implicated in bacterial iron uptake.
Authors: Xu, Q. / Rawlings, N.D. / Farr, C.L. / Chiu, H.J. / Grant, J.C. / Jaroszewski, L. / Klock, H.E. / Knuth, M.W. / Miller, M.D. / Weekes, D. / Elsliger, M.A. / Deacon, A.M. / Godzik, A. / ...Authors: Xu, Q. / Rawlings, N.D. / Farr, C.L. / Chiu, H.J. / Grant, J.C. / Jaroszewski, L. / Klock, H.E. / Knuth, M.W. / Miller, M.D. / Weekes, D. / Elsliger, M.A. / Deacon, A.M. / Godzik, A. / Lesley, S.A. / Wilson, I.A.
History
DepositionMay 28, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 10, 2011Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: imelysin peptidase
B: imelysin peptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,50614
Polymers79,9282
Non-polymers57812
Water21,4561191
1
A: imelysin peptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1726
Polymers39,9641
Non-polymers2085
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: imelysin peptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3348
Polymers39,9641
Non-polymers3707
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)131.470, 49.930, 128.320
Angle α, β, γ (deg.)90.000, 117.580, 90.000
Int Tables number5
Space group name H-MC121
DetailsCRYSTAL PACKING SUGGESTS THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

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Components

#1: Protein imelysin peptidase


Mass: 39963.996 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides ovatus (bacteria) / Strain: ATCC 8483 / Gene: BACOVA_03801 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: A7M120
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1191 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT (RESIDUES 25-384) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THE CONSTRUCT (RESIDUES 25-384) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.33 %
Description: DATA WERE SCALED USING XSCALE WITH FRIEDEL PAIRS KEPT AS SEPARATE WHEN COMPUTING R-SYM, COMPLETENESS AND
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.7
Details: 0.20M MgAcetate, 20.00% PEG-3350, No Buffer pH 7.7, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837,0.97947,0.97901
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 7, 2010 / Details: FLAT MIRROR (VERTICAL FOCUSING)
RadiationMonochromator: SINGLE CRYSTAL SI(111) BENT MONOCHROMATOR (HORIZONTAL FOCUSING)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979471
30.979011
ReflectionResolution: 1.44→29.738 Å / Num. obs: 132203 / % possible obs: 94.5 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 17.26 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 10.1
Reflection shellResolution: 1.44→1.49 Å / Rmerge(I) obs: 0.92 / Mean I/σ(I) obs: 1.2 / % possible all: 88.1

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PHENIXrefinement
SHELXphasing
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
BUSTER2.8.0refinement
RefinementMethod to determine structure: MAD / Resolution: 1.44→29.738 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.953 / Occupancy max: 1 / Occupancy min: 0.2 / Cross valid method: THROUGHOUT / σ(F): 0
Details: 1. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED ...Details: 1. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 2. MAGNESIUM (MG), CHLORIDE (CL), ETHYLENE GLYCOL (EDO) MODELED ARE PRESENT CRYSTALLIZATION/PURIFICATION/CRYO BUFFERS. 3. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5. RAMACHANDRAN OUTLIER IS LOCATION IN A REGION WITH POOR DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.19 6661 5.04 %RANDOM
Rwork0.167 ---
obs0.168 132168 --
Displacement parametersBiso mean: 31.56 Å2
Baniso -1Baniso -2Baniso -3
1-4.185 Å20 Å2-4.206 Å2
2---2.317 Å20 Å2
3----1.868 Å2
Refinement stepCycle: LAST / Resolution: 1.44→29.738 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5482 0 33 1191 6706
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.015921HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.748132HARMONIC3.5
X-RAY DIFFRACTIONt_dihedral_angle_d2067SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes199HARMONIC2
X-RAY DIFFRACTIONt_gen_planes891HARMONIC5
X-RAY DIFFRACTIONt_it5921HARMONIC20
X-RAY DIFFRACTIONt_nbd4SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.25
X-RAY DIFFRACTIONt_other_torsion15.72
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion796SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact8356SEMIHARMONIC4
LS refinement shellResolution: 1.44→1.48 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 460 4.91 %
Rwork0.243 8915 -
all0.244 9375 -
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.2239-0.5049-0.06590.56310.19480.38950.06150.01170.2631-0.0427-0.0029-0.1316-0.05280.0305-0.0586-0.057600.0213-0.06860.00130.0161-4.2036.922101.8008
23.7366-1.4581-2.26541.33190.6921.99850.19740.5194-0.1841-0.2853-0.4056-0.129-0.0498-0.16050.2081-0.1730.0750.0835-0.06350.0213-0.1299-17.95813.093570.3671
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A33 - 384
2X-RAY DIFFRACTION2{ B|* }B31 - 384

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